Mutation Annotation tool for mutation pathogenicity classification To work with notebooks please use jupyter. First install dbnsfp_annotation package, then mutant. Models are attached to the repository.
python setup.py installOR
pip install -e .from mutant.classifier import add_mutant_annotation
# example, annotate vcf, genome version hg19 (this vcf file are not attached)
add_mutant_annotation('TCGA-A1-A0SB.vcf', file_type='vcf', genome_version = 'hg19', development_mode=True, method='predict_proba')
# example, annotate maf, genome version hg38
add_mutant_annotation('TCGA-A1-A0SB.maf', file_type='maf', genome_version = 'hg38', development_mode=True, method='predict_proba')
# convert maf DNP to SNP and annotate, genome version hg38
add_mutant_annotation('TCGA-A1-A0SB.maf', file_type='maf', genome_version = 'hg38', dnp_convert_info=True, method='predict_proba')
# After annotation you will get «DNP_Converted» column in your maf with True or False values,
# where True means that DNP was converted to SNP while annotation,
# False - DNP could not be converted to SNP because of for amino acid change it need in two or more changes in codon.